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Detailed information for vg0322577580:

Variant ID: vg0322577580 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 22577580
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.03, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TCATATCCGTGGGACATGCCATATCAGCGCCACATAGGATCCTGAAGGGGCTGTGGTGATTTCGGACCTAGATGACACACTATGACAAGTTCTGGGACTT[G/A]
GATATGCATTTTGAGAGTTTAAGGATCTAGATGATACACCGCTATAAGTTTAAGGACCGCCCGTGCACCTTAATCATTACTAAAAGTGCGTAGCTAGGGT

Reverse complement sequence

ACCCTAGCTACGCACTTTTAGTAATGATTAAGGTGCACGGGCGGTCCTTAAACTTATAGCGGTGTATCATCTAGATCCTTAAACTCTCAAAATGCATATC[C/T]
AAGTCCCAGAACTTGTCATAGTGTGTCATCTAGGTCCGAAATCACCACAGCCCCTTCAGGATCCTATGTGGCGCTGATATGGCATGTCCCACGGATATGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.10% 29.90% 0.06% 0.00% NA
All Indica  2759 57.40% 42.50% 0.11% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 23.40% 76.60% 0.00% 0.00% NA
Indica I  595 96.10% 3.70% 0.17% 0.00% NA
Indica II  465 26.00% 74.00% 0.00% 0.00% NA
Indica III  913 50.50% 49.50% 0.00% 0.00% NA
Indica Intermediate  786 54.60% 45.20% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0322577580 G -> A LOC_Os03g40610.1 upstream_gene_variant ; 3572.0bp to feature; MODIFIER silent_mutation Average:36.679; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N
vg0322577580 G -> A LOC_Os03g40610-LOC_Os03g40630 intergenic_region ; MODIFIER silent_mutation Average:36.679; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0322577580 NA 2.85E-13 Grain_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0322577580 NA 4.48E-23 Grain_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0322577580 NA 4.61E-06 mr1043 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0322577580 NA 3.31E-07 mr1193 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0322577580 NA 2.94E-10 mr1291 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0322577580 NA 1.40E-06 mr1502 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0322577580 NA 2.88E-06 mr1815 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0322577580 NA 3.94E-07 mr1892 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0322577580 NA 9.12E-07 mr1024_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0322577580 NA 1.40E-07 mr1120_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0322577580 NA 5.01E-07 mr1247_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0322577580 NA 1.74E-06 mr1632_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251